Data Loading & 3D Visualization
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1 Neuroimage Analysis Center Data Loading & 3D Visualization Sonia Pujol, Ph.D. Surgical Planning Laboratory Harvard Medical School Leonardo da Vinci ( ), Virgin and Child Alte Pinakothek, München
2 Slicer3 An end-user application for image analysis An open-source environment for software development A software platform that is both easy to use for clinical researchers and easy to extend for programmers
3 Slicer3 Slicer3 is a multi-platform software that is developed and maintained on: Windows XP Linux x86_64 Linux x86 Mac OSX Darwin x86-intel
4 3D Visualization dataset This course is built upon three datasets of a single healthy subject brain: MR DICOM GRASS MR Nrrd SPGR Pre-computed Label Map
5 Learning objective Following this tutorial, you ll be able to load and visualize volumes within Slicer3, and to interact in 3D with structural images and models.
6 Start Slicer3 Linux/Mac users Launch the Slicer3 executable located in the Slicer3.6 directory Windows users Select Start All Programs Slicer Slicer3
7 Slicer Welcome The SlicerWelcome module is the module displayed by default. This module gives an overview of the GUI of Slicer3, and data loading & saving functionalities.
8 The Graphical User Interface (GUI) of Slicer3.6 integrates 8 main components: the File Menu the Menu Toolbar the Module GUI Panel the 3D Viewer the Slice Viewer the Slice Controller the 3D View Controller File Menu Module GUI Panel Slice Controller 3DView Controller Slicer3 GUI Menu Toolbar 3DViewer Slice Viewer Progress and Error Log
9 Overview Part 1. Loading and visualizing multiple volumes simultaneously Part 3. Visualizing 3D reconstructions of anatomical surfaces Part 2. Loading and visualizing segmented structures overlaid on grayscale images Part 4. The lightbox viewer Part 5. Saving data
10 Data Representation j k i The result of a volumetric acquisition is a 3D volume of data related to the patient. The 3D raster dataset is sampled on a discrete grid with elements called voxels which contain the signal intensity.
11 Part 1: Loading and visualizing multiple volumes simultaneously
12 Select File Add Volume from the file menu. Loading Volumes
13 Loading Volumes Browse to the location of the Slicer3VisualizationDataset directory
14 Loading Volumes Select the file 001.dcm in the /dicom directory
15 Loading Volumes Slicer displays the Dicom header information of the images. Browse through the Dicom information panel to display the dimensions of the images.
16 Loading Volumes Image dimensions: Rows = 256, Columns = 256
17 Loading Volumes Click on Apply to load the Dicom volume in Slicer.
18 Loading Volumes The Dicom images appear in the Background display of the 2DViewer.
19 Loading Volumes Left click on the menu Modules and select All Modules to display the list of 95 modules available for image analysis and 3D visualization. Select the module Volumes
20 Loading Volumes The panel of the module Volumes appears in the interface. Click on the panel Display
21 Loading Volumes Use the Window/Level slider to adjust the display of the MR images.
22 Loading Volumes Select File Add Volume
23 Loading Volumes Browse to find the header file of the spgr volume spgr.nhdr located in the directory Slicer3VisualizationDataset/nrrd and click on Open.
24 Loading Volumes Select Image Origin Centered and click on Apply to load the volume spgr.nhdr
25 Loading Volumes The spgr volume appears in the Background display of the 2D Viewer.
26 Exploring the data Click on the choose view icon
27 Exploring the data Select the red slice only layout from the menu
28 Exploring the data The axial slices of the spgr volume appear in the 3D viewer. Click on the icon slices fit to window to adjust the dimensions of the image to the size of the window.
29 To simultaneously view the dicom and the nrrd volumes, left click on the drop-down menu to the right of the Foreground icon and select the image 001.dcm Exploring the data
30 Click on the Background icon or the Foreground icon to display the spgr or the DICOM volumes in the Viewer Exploring the data
31 Exploring the data Browse the images using the slider to display the ventricles (~slice 38)
32 Exploring the data Click on the conventional layout icon to come back to the standard view
33 Loading Volumes Click on the icon slices fit to window to adjust the dimensions of the image to the size of the window.
34 Part 2: Loading and visualizing segmented structures overlaid on grayscale images
35 Label map Image segmentation is the extraction of structural information of particular interest from surrounding image. Each pixel is assigned a specific label value which corresponds to the anatomical structure that it belongs to. The three-dimensional result of the segmentation is a binary array called a label map.
36 Click on Select Volume File Loading a label map
37 Loading a label map Browse to find the header file all.nhdr of the label map dataset located in the directory Slicer3VisualizationDataset/nrrd and click on Open
38 Visualizing a label map Set Image Origin to Centered Check the Label Map box and click on Apply
39 Slicer displays the label map all in the Label layer Visualizing a label map Click on the links icon.
40 Visualizing Multiple Volumes Label Viewer Left click the dropdown menu to the right of the L icon and select None
41 Visualizing Multiple Volumes Foreground Viewer Left click on the dropdown menu to the right of the F icon and select the volume all
42 Visualizing Multiple Volumes Select Manipulate Slice Views Use the slider to fade between the labelmap all (Foreground) and the spgr volume (Background).
43 3D Visualization Select the module Data in the module menu
44 3D Visualization The Data module displays the volumes loaded in the current Slicer Scene.
45 3D Visualization The Load & Add Scene tab displays the different data types that can be added to the scene.
46 3D Visualization Click on the links icon. Slicer Click on displays the Slice 2D anatomical Visibility slices icon in to the 3D display viewer the slices in the 3D Viewer
47 3D Visualization Slicer displays 2D anatomical slices in the 3D viewer
48 3D Visualization Position the mouse in the 3D Viewer, hold down the left mouse button and drag to rotate the volumes
49 Part 3: Loading and visualizing 3D models of the anatomy
50 3D models A 3D model is a surface reconstruction of an anatomical structure. The model is a triangular mesh that approximates a surface from a 3D label map. The scalar values for surface models are integers which correspond to the label that had been assigned in the segmentation process.
51 3D Visualization Click on the left icon in Add data or data directory
52 3D Visualization A small window displays information on how to use the function Add data or data directory Click on the icon
53 3D Visualization Click on Add Directory to select the directory Slicer3VisualizationDataset
54 Loading 3D models Select the directory Slicer3VisualizationDataset/models and click on OK
55 Loading 3D models The list of elements present in the models directory appears in the Add Data window. Click on Apply to load all the 3D models.
56 Loading 3D models Slicer loads the 3D models in the 3D Viewer. The models have been added to the MRML scene.
57 Loading a 3D model Select the module Models Click on the panel Hierarchy & Display to access the module s display components
58 Select the model Skin.vtk Click on the icon Set Color and choose a new color for the 3D model of the head. Visualizing a 3D model
59 Visualizing a 3D model Change the opacity of the skin model from 1.0 to 0.5 using the opacity slider:
60 Visualizing a 3D model The 3D models of the brain and vessels appear through the skin
61 Visualizing a 3D model Turn off the visibility of the skin model
62 Visualizing a 3D model Select the model Brain and change its color to white
63 Visualizing a 3D model Select Green Slice Only Layout from the Viewer menu
64 Visualizing a 3D model Click on the icon to adjust the size of the image to the size of the window.
65 Visualizing a 3D model Select Slice Intersection Visible to display the model intersection on the slice plane.
66 Visualizing a 3D model The intersection of the 3D model of the brain with the 2D image plane appears in the viewer. Go back to the conventional layout
67 Visualizing a 3D model Select the model Vessels and change its color to red
68 Visualizing a 3D model Select the model Brain and select the option Clipping
69 Visualizing a 3D model Set Yellow Slice Clipping to Positive Space
70 Visualizing a 3D model Click on the letter S in the Control Window to display a superior view of the 3D models
71 Visualizing a 3D model Use the yellow slice slider to expose the 3D model of the vasculature
72 Visualizing a 3D model Turn off the option clipping for the model Brain and set the Yellow Slice Clipping to Off Turn on the visibility of the model Skin
73 Visualizing a 3D model Slicer displays the 3D models of the Skin, Vessels and Brain.
74 Part 4: Lightbox viewer
75 Visualizing a 3D model Select the option Compare Layout in the Viewer menu
76 Visualizing a 3D model Set the Number of compare Viewers to 1 and the number of lightbox rows and columns to 2 Click on Apply
77 Lightbox viewer Slicer displays a lightbox view of the Background dataset.
78 Lightbox viewer Browse through the spgr volume using the lightbox slider
79 Lightbox viewer Slicer displays 4 adjacent axial slices of the spgr volume simultaneously
80 Lightbox viewer Left click on the Slice Viewer menu of the Compare Layout viewer
81 Lightbox viewer Select the lightbox view option
82 Lightbox viewer Set the configuration of the light box view to 6x6
83 Lightbox viewer Slicer displays a matrix of 36 adjacent axial slices of the spgr volume.
84 Lightbox viewer Select the option Conventional Layout in the Viewer menu
85 Part 5: Loading and saving a Scene
86 Saving Data Click on File and Select Save
87 Saving Data The list of elements currently loaded into Slicer3 appears. Make sure only the first check box is selected
88 Click on Change Destination for All Selected and browse to the location where the scene will be saved Saving Data
89 Saving Data Browse to the directory where you would like to save your scene and click OK
90 Double click on the file name SlicerScene1 and change it to Slicer3DScene Saving Data
91 Saving Data Click on Save Selected
92 Creating Scene Snapshots Choose a 3D view of the scene and click on the capture snapshot icon
93 Creating Scene Snapshots Enter the Snapshot name MySceneSnapshot1 and click on OK
94 Creating Scene Snapshots Select a Superior view of the dataset, and click on the capture snapshot icon
95 Creating Scene Snapshots Enter the name MySceneSnapshot2 and click on OK
96 Creating Scene Snapshots Select File Save and click on Save Selected to include the two scene snapshots in the saved scene
97 Creating Scene Snapshots Click Yes to overwrite the file with a new file that contains the scene snapshots
98 Saving Data Select File Close Scene in the main menu and click on OK
99 Saving Data The elements of the previous scene disappear from the Viewer.
100 Saving Data Select File Load Scene from the main menu
101 Saving Data Browse to find the file Slicer3DScene.mrml and click on Open
102 Loading a Scene Slicer loads the elements from the scene Slicer3DScene.mrml
103 Loading a Scene Left-click on the restore snapshot icon. Select MySceneSnapshot2 and click on restore
104 Loading a Scene Slicer restores the scene snapshot MySceneSnapshot2
105 Conclusion 3D visualization of anatomical surface reconstructions 3D interaction with volumes and models Open-source platform
106 Acknowledgments NIH U54EB Neuroimage Analysis Center NIH P41RR013218
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